It would be handy in the IDE to be able to redirect serial input/ouput in the serial monitor window to/from other files.

For instance, when using Serial.print () to generate debugging data, it is sometimes useful to gather that data in a file to plot or analyze. Currently there is no way to pause/continue the serial monitor window (see this suggestion). This makes it hard, other than by disconnecting the USB cable, to grab text data from the monitor window.

The Arduino's IDE serial monitor is a very basic but useful tool. They have added a few features along the way like seperate window in version 17, but it will most likely never be developed to suit all needs by all people.

It really is better if you wish many more advance commands like file store or file transmit, macro sending, etc, to utilize a more powerful general purpose PC based serial terminal program. If you are using Windows I can highly recommend the Brey terminal program, it's very powerful and free. It's a standalone EXE application requiring no DLL or other installation headaches. I also carry a copy in a USB memory clip.

Correct, works great. Just remember to disconnect the port on the terminal program before reusing or launching the Arduino IDE and reconnecting to the port after you have uploaded a sketch from the IDE. There is a connect/disconnect button of the Brey terminal program's GUI. No need to close the Arduino IDE, you can leave it opened as well as the terminal program. The key is that the Arduino IDE is well behaved about disconnecting from the USB comm channel automatically once it is done with the upload command.

The bray terminal GUI even has a handy DTR button so you can reset the attached Arduino board just by clicking it any time you want to force a reset to the attached Arduino board.